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A Genomic Epidemiology Study of Multidrug-Resistant Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii in Two Intensive Care Units in Hanoi, Vietnam
23 Pages Posted: 28 Sep 2021
More...Abstract
Background: Vietnam has high rates of antimicrobial resistance (AMR) but limited capacity for genomic surveillance. This study used whole genome sequencing (WGS) to examine the prevalence and transmission of three key AMR pathogens in two intensive care units in Hanoi, Vietnam.
Methods: A prospective surveillance study of all adults admitted to intensive care units (ICUs) at the National Hospital for Tropical Diseases (NHTD) and Bach Mai Hospital (BMH) was conducted between June 2017 and January 2018. Clinical and environmental samples were cultured on selective media, characterised using MALDI TOF MS, and illumina sequenced. Phylogenies based on the de novo assemblies (SPAdes) were constructed using Mafft (PARsnp), Gubbins and RAxML. Resistance genes were detected using Abricate against the NCBI database.
Findings: 3,153 Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii isolates from 369 patients were analysed. Phylogenetic analysis revealed predominant lineages within A. baumannii (global clone [GC]2, sequence types [ST]2, ST571) and K. pneumoniae (ST15, ST16, ST656, ST11, ST147) isolates. Colonisation was most common with E. coli (88.9%) followed by K. pneumoniae (62.4%). Of the E. coli, 91% carried a blaCTX-M variant, while 81% of K. pneumoniae isolates carried blaNDM (54%) and/or blaKPC (45%). Transmission analysis using single nucleotide polymorphisms (SNPs) identified 167 clusters involving 251 (68%) patients, in some cases involving patients from both ICUs. There were no significant differences between the lineages or AMR genes recovered between the two ICUs.
Interpretation: This study represents the largest prospective surveillance study of key AMR pathogens in Vietnamese ICUs. Clusters of closely related isolates in patients across both ICUs suggests recent transmission prior to ICU admission in other healthcare settings or in the community.
Funding Information: This study was funded by the UK Medical Research Council Newton Fund (grant MR/N029399/1); the Ministry of Science and Technology, Vietnam (grant HNQT/SPÐP/04.16) and the Wellcome Trust (grant 206194). LWR is supported by EMBL-EBI biomedical postdoctoral research fellowship. MET was supported by a Clinician Scientist Fellowship (funded by the Academy of Medical Sciences and the Health Foundation) and the National Institutes of Health Research Cambridge Biomedical Research Centre.
Declaration of Interests: All authors declare no conflicts of interest.
Ethics Approval Statement: The study protocol was approved by the Scientific and Ethical Committees of the National Hospital for Tropical Diseases and Bach Mai Hospital and by the University of Cambridge Human Biology and Research Ethics Committee (reference: HBREC 2017.09). Written informed consent was obtained from the patient or from their relative prior to enrolment in the study.
Keywords: antimicrobial resistance, multidrug-resistant, whole genome sequencing, E. coli, K. pneumoniae, A. baumannii, transmission, intensive care, Vietnam
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